I have accidentally aligned a large amount of samples to a reference genome that includes patch chromsomes (specifically, using GRCh38.p5. According to the STAR manual I should only have used the major chromosomes and un-placed and un-localized chromosomes (which I think is GRCh38.
However, I do not know how bad it is. Some reads will go to genes on the patched chromosomes, could I assign these to the same gene that is located on the main chromosomes? Or is the only way to fix it to realign to the correct chromosome?